On Thu, Apr 23, 2009 at 3:59 PM, Francesco Pietra <chiendar...@gmail.com>wrote:
> hi:
> with script
>
> data = open('134-176_rectified_edited.pdb', 'r')
> outp = open('134-176_renumbered.pdb', 'w')
>
> for L in data:
> if L[3] == 'M':
> L = L[:24] + "%4d" % (int(L[24-28])+133) + L[28:]
> outp.write(L)
>
>
> i wanted to modify lines of the type:
> ATOM 1 HH31 ACE 1 1.573 1.961 0.769 1.00 0.00
> H
>
> to add 133 to column 25, getting 134 there, and so on for next lines 2
> -> 135, 3 -> 136, etc.
>
>
> i must have heavily messed things because the file was not even read:
>
> $ python renumber.py 134-176_rectified.pdb
> Traceback (most recent call last):
> File "renumber.py", line 6, in <module>
> L = L[:24] + "%4d" % (int(L[24-28])+133) + L[28:]
> ValueError: invalid literal for int() with base 10: ''
>
>
>
> thanks for having an expert look
>
> chiendarret
> --
> http://mail.python.org/mailman/listinfo/python-list
>
I wrote this function the other day for something similar I needed to do,
you may find it useful:
def chunk_line(line, steps):
"""Return a list of chunks from a string, with sizes as specified by the
list steps.
>>> line = '1121231234'
>>> steps = [1,2,3,4]
>>> chunk_line(line, steps)
['1', '12', '123', '1234']
"""
result = []
for step in steps:
result.append(line[:step])
line = line[step:]
return result
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